Structure, inter-annual recurrence, and global-scale connectivity of airborne microbial communities

A review of pathogenic airborne fungi and bacteria: unveiling occurrence, sources, and profound human health implication

Airborne fungi and bacteria have been extensively studied by researchers due to their significant effects on human health. We provided an overview of the distribution and sources of airborne pathogenic microbes, and a detailed description of the detrimental effects that these microorganisms cause to human health in both outdoor and indoor environments. By analyzing the large body of literature published in this field, we offered valuable insights into how airborne microbes influence our well-being. The findings highlight the harmful consequences associated with the exposure to airborne fungi and bacteria in a variety of natural and human-mediated environments. Certain demographic groups, including children and the elderly, immunocompromised individuals, and various categories of workers are particularly exposed and vulnerable to the detrimental effect on health of air microbial pollution. A number of studies performed up to date consistently identified Alternaria, Cladosporium, Penicillium, Aspergillus, and Fusarium as the predominant fungal genera in various indoor and outdoor environments. Among bacteria, Bacillus, Streptococcus, Micrococcus, Enterococcus, and Pseudomonas emerged as the dominant genera in air samples collected from numerous environments. All these findings contributed to expanding our knowledge on airborne microbe distribution, emphasizing the crucial need for further research and increased public awareness. Collectively, these efforts may play a vital role in safeguarding human health in the face of risks posed by airborne microbial contaminants.

Aerosol sources and transport paths co-control the atmospheric bacterial diversity over the coastal East China Sea

Airborne bacteria along with chemical composition of aerosols were investigated during five sampling seasons at an offshore island of the East China Sea. Bacterial diversity was the lowest in spring, the highest in winter, and similar between the autumns of 2019 and 2020, suggesting remarkably seasonal variation but little interannual change. Geodermatophilus (Actinobacteria) was the indicator genus of mineral dust (MD) showed higher proportion in spring than in other seasons. Mastigocladopsis_PCC-10914 (Cyanobacteria) as the indicator of sea salt (SS) demonstrated the highest percentages in both autumns, when the air masses mainly passed over the ocean prior to the sampling site. The higher proportions of soil-derived genera Rubellimicrobium and Craurococcus (both Proteobacteria) and extremophile Chroococcidiopsis_SAG_2023 (Cyanobacteria) were found in summer and winter, respectively. Our study explores the linkage between aerosol source and transport path and bacterial composition, which has implication to understanding of land-sea transmission of bacterial taxa.

Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain)

Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.

Fog caused distinct diversity of airborne bacterial communities enriched with pathogens over central Indo-Gangetic plain in India

Fog causes enhancement of bacterial loading in the atmosphere. Current study represents the impact of occurrences of fog on the alteration of diversity of airborne bacteria and their network computed from metagenomic data of airborne samples collected at Arthauli (25.95°N, 85.10°E) situated at central Indo-Gangetic Plain (IGP) during 1-14 January 2021. A distinct bacterial diversity with a complex network is identified in foggy condition due to the enrichment of unique types of bacteria. Present investigation highlights a statistically significant enrichment of airborne pathogenic bacteria found in a unique ecosystem within air evolved due to the occurrences of fog over central IGP. In the foggy network, Cutibacterium, an opportunistic pathogen, is identified to be interacting maximum (21 edges) with other bacteria with statistically significant copresence relation, which are responsible for various infections for human beings. A 40-60% increase (p < 0.01) in the abundance of pathogenic bacteria for respiratory and skin diseases is noticed in fog period. Among the fog-enriched bacteria, Cutibacterium, Herbaspirillum, Paenibacillus, and Tsukamurella are examples of opportunistic bacteria causing various respiratory diseases, while Paenibacillus can even cause skin cancer and acute lymphoblastic leukemia.

Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere

Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.

Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China

Soil microorganisms play vital roles in regulating multiple ecosystem functions. Recent studies have revealed that the rare microbial taxa (with extremely low relative abundances, which are still largely ignored) are also crucial in maintaining the health and biodiversity of the soil and may respond differently to environmental pressure. However, little is known about the soil community structures of abundant and rare taxa and their assembly processes in different soil layers on the Qinghai-Tibet Plateau (QTP). The present study investigated the community structure and assembly processes of soil abundant and rare microbial taxa on the northeastern edge of the QTP. Soil microbial abundance was defined by abundant taxa, whereas rare taxa contributed to soil microbial diversity. The results of null model show that the stochastic process ruled the assembly processes of all sub-communities. Dispersal limitation contributed more to the assembly of abundant microbial taxa in the different soil layers. In contrast, drift played a more critical role in the assembly processes of the rare microbial taxa. In addition, in contrast to previous studies, the abundant taxa played more important roles in co-occurrence networks, most likely because of the heterogeneity of the soil, the sparsity of amplicon sequencing, the sampling strategy, and the limited samples in the present study. The results of this study improve our understanding of soil microbiome assemblies on the QTP and highlight the role of abundant taxa in sustaining the stability of microbial co-occurrence networks in different soil layers.

The atmosphere: a transport medium or an active microbial ecosystem?

The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.

Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient

INTRODUCTION

The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica.

METHODS

We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons.

RESULTS AND DISCUSSION

Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.

The waterbodies of the halo-volcanic Dallol complex: earth analogs to guide us, where to look for life in the universe

Microbes are the Earth life forms that have the highest degree of adaptability to survive, live, or even proliferate in very hostile environments. It is even stated that microbes can cope with any extreme physico-chemical condition and are, therefore, omnipresent all over the Earth: on all the continents, inside its crust and in all its waterbodies. However, our study suggests that there exists areas and even water rich environments on Earth where no life is possible. To support the fact that water rich environments can be lifeless, we performed an extensive survey of 10 different hyper extreme waterbodies of the halo-volcanic Dallol complex (Danakil depression, Ethiopia, Horn of Africa). In our study, we combined physico-chemical analyses, mineralogical investigations, XRD and SEM-EDX analyses, ATP measurements, 16S rDNA microbial community determinations, and microbial culturing techniques. According to our findings, we suggest that the individual physico-chemical parameters, water activity, and kosmo-chaotropicity, are the two most important factors that determine whether an environment is lifeless or capable of hosting specific extreme lifeforms. Besides, waterbodies that contained saturated levels of sodium chloride but at the same time possessed extreme low pH values, appeared to be poly-extreme environments in which no life could be detected. However, we clearly discovered a low diversity microbial community in waterbodies that were fully saturated with sodium chloride and only mildly acidic. Our results can be beneficial to more precisely classify whole or certain areas of planetary bodies, including water rich environments, as either potentially habitable or factual uninhabitable environments.

The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome

The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.

Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments

Even though thermophiles are best known from geothermal and other heated systems, numerous studies have demonstrated that they occur ubiquitously in mesothermal and permanently cold soils and sediments. Cultivation based studies of the latter have revealed that the thermophiles within them are mostly spore-forming members of the Firmicutes. Since the geographic distribution of spores is presumably unconstrained by transport through the atmosphere, similar communities (composition and diversity) of thermophiles might be expected to emerge in mesothermal habitats after they are heated. Alternatively, thermophiles might experience environmental selection before or after heating leading to divergent communities. After demonstrating the ubiquity of anaerobic thermophiles and CO uptake in a variety of mesothermal habitats and two hot springs, we used high throughput sequencing of 16S rRNA genes to assess the composition and diversity of populations that emerged after incubation at 60°C with or without headspace CO concentrations of 25%. Anaerobic Firmicutes dominated relative abundances at most sites but anaerobic thermophilic members of the Acidobacteria and Proteobacteria were also common. Nonetheless, compositions at the amplicon sequence variant (ASV) level varied among the sites with no convergence resulting from heating or CO addition as indicated by beta diversity analyses. The distinctions among thermophilic communities paralleled patterns observed for unheated "time zero" mesothermal soils and sediments. Occupancy analyses showed that the number of ASVs occupying each of n sites decreased unimodally with increasing n; no ASV occupied all 14 sites and only one each occupied 11 and 12 sites, while 69.3% of 1873 ASVs occupied just one site. Nonetheless, considerations of distances among the sites occupied by individual ASVs along with details of their distributions indicated that taxa were not dispersal limited but rather were constrained by environmental selection. This conclusion was supported by βMNTD and βNTI analyses, which showed dispersal limitation was only a minor contributor to taxon distributions.

Aerobiology over the Southern Ocean - Implications for bacterial colonization of Antarctica

Parts of the Antarctic are experiencing dramatic ecosystem change due to rapid and record warming, which may weaken biogeographic boundaries and modify dispersal barriers, increasing the risk of biological invasions. In this study, we collected air samples from 100 locations around the Southern Ocean to analyze bacterial biodiversity in the circumpolar air around the Antarctic continent, as understanding dispersal processes is paramount to assessing the risks of microbiological invasions. We also compared the Southern Ocean air bacterial biodiversity to non-polar ecosystems to identify the potential origin of these Southern Ocean air microorganisms. The bacterial diversity in the air had both local and global origins and presented low richness overall but high heterogeneity, compatible with a scenario whereby samples are composed of a suite of different species in very low relative abundances. Only 4% of Amplicon Sequence Variants (ASVs) were identified in both polar and non-polar air masses, suggesting that the polar air mass over the Southern Ocean can act as a selective dispersal filter. Furthermore, both microbial diversity and community structure both varied significantly with meteorological data, suggesting that regional bacterial biodiversity could be sensitive to changes in weather conditions, potentially altering the existing pattern of microbial deposition in the Antarctic.

Infectious Diseases Associated with Desert Dust Outbreaks: A Systematic Review

Background: Desert dust outbreaks and dust storms are the major source of particulate matter globally and pose a major threat to human health. We investigated the microorganisms transported with desert dust particles and evaluated their potential impact on human health. Methods: A systematic review of all reports on the association between non-anthropogenic desert dust pollution, dust microorganisms and human health is conducted. Results: In total, 51 articles were included in this review. The affected regions studied were Asia (32/51, 62.7%) followed by Europe (9/51, 17.6%), America (6/51, 11.8%), Africa (4/51, 7.8%) and Australia (1/51, 2.0%). The Sahara Desert was the most frequent source of dust, followed by Asian and American deserts. In 39/51 studies the dust-related microbiome was analyzed, while, in 12/51 reports, the association of desert dust with infectious disease outbreaks was examined. Pathogenic and opportunistic agents were isolated from dust in 24/39 (61.5%) and 29/39 (74.4%) of the studies, respectively. A significant association of dust events with infectious disease outbreaks was found in 10/12 (83.3%) reports. The infectious diseases that were mostly investigated with dust outbreaks were pneumonia, respiratory tract infections, COVID-19, pulmonary tuberculosis and coccidioidomycosis. Conclusions: Desert dust outbreaks are vehicles of a significant number of pathogenic or opportunistic microorganisms and limited data indicate an association between dust events and infectious disease outbreaks. Further research is required to strengthen the correlation between dust events and infectious diseases and subsequently guide preventive public health measures.

Bacterial Colonisation: From Airborne Dispersal to Integration Within the Soil Community

The deposition of airborne microorganisms into new ecosystems is the first stage of colonisation. However, how and under what circumstances deposited microorganisms might successfully colonise a new environment is still unclear. Using the Arctic snowpack as a model system, we investigated the colonisation potential of snow-derived bacteria deposited onto Arctic soils during and after snowmelt using laboratory-based microcosm experiments to mimic realistic environmental conditions. We tested different melting rate scenarios to evaluate the influence of increased precipitation as well as the influence of soil pH on the composition of bacterial communities and on the colonisation potential. We observed several candidate colonisations in all experiments; with a higher number of potentially successful colonisations in acidoneutral soils, at the average snowmelt rate measured in the Arctic. While the higher melt rate increased the total number of potentially invading bacteria, it did not promote colonisation (snow ASVs identified in the soil across multiple sampling days and still present on the last day). Instead, most potential colonists were not identified by the end of the experiments. On the other hand, soil pH appeared as a determinant factor impacting invasion and subsequent colonisation. In acidic and alkaline soils, bacterial persistence with time was lower than in acidoneutral soils, as was the number of potentially successful colonisations. This study demonstrated the occurrence of potentially successful colonisations of soil by invading bacteria. It suggests that local soil properties might have a greater influence on the colonisation outcome than increased precipitation or ecosystem disturbance.

Short-range contributions of local sources to ambient air

Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m² tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.

Active Microbial Airborne Dispersal and Biomorphs as Confounding Factors for Life Detection in the Cell-Degrading Brines of the Polyextreme Dallol Geothermal Field

Determining the precise limits of life in polyextreme environments is challenging. Studies along gradients of polyextreme conditions in the Dallol proto-volcano area (Danakil salt desert, Ethiopia) showed the occurrence of archaea-dominated communities (up to 99%) in several hypersaline systems but strongly suggested that life did not thrive in the hyperacidic (pH ∼0), hypersaline (∼35% [wt/vol],) and sometimes hot (up to 108°C) ponds of the Dallol dome. However, it was recently claimed that archaea flourish in these brines based on the detection of one Nanohaloarchaeotas 16S rRNA gene and fluorescent in situ hybridization (FISH) experiments with archaea-specific probes. Here, we characterized the diversity of microorganisms in aerosols over Dallol, and we show that, in addition to typical bacteria from soil/dust, they transport halophilic archaea likely originating from neighboring hypersaline ecosystems. We also show that cells and DNA from cultures and natural local halophilic communities are rapidly destroyed upon contact with Dallol brine. Furthermore, we confirm the widespread occurrence of mineral particles, including silica-based biomorphs, in Dallol brines. FISH experiments using appropriate controls show that DNA fluorescent probes and dyes unspecifically bind to mineral precipitates in Dallol brines; cellular morphologies were unambiguously observed only in nearby hypersaline ecosystems. Our results show that airborne cell dispersal and unspecific binding of fluorescent probes are confounding factors likely affecting previous inferences of archaea thriving in Dallol. They highlight the need for controls and the consideration of alternative abiotic explanations before safely drawing conclusions about the presence of life in polyextreme terrestrial or extraterrestrial systems.

Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape

In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbor a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems. This article is protected by copyright. All rights reserved.

A framework for integrating microbial dispersal modes into soil ecosystem ecology

Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships.

Isolation, Characterization, and Antimicrobial Activity of Bacterial and Fungal Representatives Associated With Particulate Matter During Haze and Non-haze Days

Particulate matter (PM) has been a threat to the environment and public health in the metropolises of developing industrial countries such as Beijing. The microorganisms associated with PM have an impact on human health if they are exposed to the respiratory tract persistently. There are few reports on the microbial resources collected from PM and their antimicrobial activities. In this study, we greatly expanded the diversity of available commensal organisms by collecting 1,258 bacterial and 456 fungal isolates from 63 PM samples. A total of 77 bacterial genera and 35 fungal genera were included in our pure cultures, with Bacillus as the most prevalent cultured bacterial genus, Aspergillus, and Penicillium as the most prevalent fungal ones. During heavy-haze days, the numbers of colony-forming units (CFUs) and isolates of bacteria and fungi were decreased. Bacillus, Paenibacillus, and Chaetomium were found to be enriched during haze days, while Kocuria, Microbacterium, and Penicillium were found to be enriched during non-haze days. Antimicrobial activity against common pathogens have been found in 40 bacterial representatives and 1 fungal representative. The collection of airborne strains will provide a basis to greatly increase our understanding of the relationship between bacteria and fungi associated with PM and human health.

OUP accepted manuscript

The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.

A long-term atmospheric baseline for intercontinental exchange of airborne pathogens

The atmosphere is a potential pathway for global-scale and long-range dispersal of viable microorganisms, promoting biological interconnections among the total environment. We aimed to provide relevant baseline information for long-range long-term intercontinental exchange of potentially infectious airborne microorganisms of major interest in environmental and health-related disciplines. We used an interannual survey (7-y) with wet depositions fortnightly collected above the boundary layer (free troposphere) at a remote high-elevation LTER (Long-Term-Ecological-Research) site, analyzed by 16S and 18S rRNA genes, and compared to a database of 475 well-known pathogens. We applied a conservative approach on close relatives of pathogenic species (>98% identity) standing their theoretical upper limit for atmospheric baseline relative abundances. We identified c. 2-3% of the total airborne microbiota as potential pathogens. Their most frequent environmental origins were soil, aquatic, and anthropogenic sources. Phytopathogens (mostly fungi) were the potential infectious agents most widely present. We uncovered consistent interannual dynamics with taxa foreseeable over time (i.e., predictable seasonal behavior) and under recurrent environmental scenarios (e.g., Saharan dust intrusions), respectively, being highly valuable microbial forensic environmental indicators. Up to 8 bacterial and 21 fungal genera consistently showed temporal abundances and recurrences unevenly distributed. Incidence of allergenic fungi was lower in summer, and significantly higher in spring. Close relatives to Coccidioides posadasii consistently showed higher signals (i.e., high specificity and high fidelity) in winter, whereas Cryptococcus neoformans had a significant signal in spring. Along Saharan dust intrusions, the bacterial phytopathogens Acidovorax avenae and Agrobacterium tumefaciens and the fungal phytopathogens Pseudozyma hubeiensis and Peniophora sp. consistently showed higher signals. Potential human pathogens showed low proportion, being mostly fungal allergens. Microorganisms related to obligated human, amphibian and fish pathogens were commonly found in winter. More studies in remote field sites above the boundary layer will unveil whether or not a similar trend is found globally.

Airborne Bacterial Community Composition According to Their Origin in Tenerife, Canary Islands

Microorganisms are ubiquitous in the environment, and the atmosphere is no exception. However, airborne bacterial communities are some of the least studied. Increasing our knowledge about these communities and how environmental factors shape them is key to understanding disease outbreaks and transmission routes. We describe airborne bacterial communities at two different sites in Tenerife, La Laguna (urban, 600 m.a.s.l.) and Izaña (high mountain, 2,400 m.a.s.l.), and how they change throughout the year. Illumina MiSeq sequencing was used to target 16S rRNA genes in 293 samples. Results indicated a predominance of Proteobacteria at both sites (>65%), followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria were the most frequent within the Proteobacteria phylum during spring and winter, while Alphaproteobacteria dominated in the fall and summer. Within the 519 genera identified, Cellvibrio was the most frequent during spring (35.75%) and winter (30.73%); Limnobacter (24.49%) and Blastomonas (19.88%) dominated in the summer; and Sediminibacterium represented 10.26 and 12.41% of fall and winter samples, respectively. Sphingomonas was also identified in 17.15% of the fall samples. These five genera were more abundant at the high mountain site, while other common airborne bacteria were more frequent at the urban site (Kocuria, Delftia, Mesorhizobium, and Methylobacterium). Diversity values showed different patterns for both sites, with higher values during the cooler seasons in Izaña, whereas the opposite was observed in La Laguna. Regarding wind back trajectories, Tropical air masses were significantly different from African ones at both sites, showing the highest diversity and characterized by genera regularly associated with humans (Pseudomonas, Sphingomonas, and Cloacibacterium), as well as others related to extreme conditions (Alicyclobacillus) or typically associated with animals (Lachnospiraceae). Marine and African air masses were consistent and very similar in their microbial composition. By contrast, European trajectories were dominated by Cellvibrio, Pseudomonas, Pseudoxanthomonas, and Sediminibacterium. These data contribute to our current state of knowledge in the field of atmospheric microbiology. However, future studies are needed to increase our understanding of the influence of different environmental factors on atmospheric microbial dispersion and the potential impact of airborne microorganisms on ecosystems and public health.

General decline in the diversity of the airborne microbiota under future climatic scenarios

Microorganisms attached to aerosols can travel intercontinental distances, survive, and further colonize remote environments. Airborne microbes are influenced by environmental and climatic patterns that are predicted to change in the near future, with unknown consequences. We developed a new predictive method that dynamically addressed the temporal evolution of biodiversity in response to environmental covariates, linked to future climatic scenarios of the IPCC (AR5). We fitted these models against a 7-year monitoring of airborne microbes, collected in wet depositions. We found that Bacteria were more influenced by climatic variables than by aerosols sources, while the opposite was detected for Eukarya. Also, model simulations showed a general decline in bacterial richness, idiosyncratic responses of Eukarya, and changes in seasonality, with higher intensity within the worst-case climatic scenario (RCP 8.5). Additionally, the model predicted lower richness for airborne potential eukaryotic (fungi) pathogens of plants and humans. Our work pioneers on the potential effects of environmental variability on the airborne microbiome under the uncertain context of climate change.

Air-dispersed aquatic microorganisms show establishment and growth preferences in different freshwater colonisation habitats

We attempted to mimic aeolian ecosystems to examine how filters posed by regional characteristics can influence the establishment and growth of airborne microcolonisers of a common air source. Using a natural single source of aerosols we applied a combined microscopy and high-throughput sequencing approach to examine the diversity, settling and growth potential of air-dispersed microbes in water containers representing newly formed aquatic colonisation habitats of different trophic states and salinity. Heterotrophic microeukaryotes were favoured as initial settlers when nutrients were low, while autotrophs rapidly proliferated in the high-nutrient containers, possibly due to favourable germinating conditions for their preferred mode of dispersal with resting spores. Following settling of colonisers, we investigated two contrasting hypotheses: if the different water colonisation habitats harboured the same microbial communities after establishment and growth periods, this would point towards a selection of best-fit cosmopolitan colonisers, regardless of habitat-specific characteristics. Alternatively, community dissimilarities after the growth period would suggest a selection of settlers due to bottom-up controls combined with priority effects. Both analyses suggested that the structure of the microbial communities in the different colonisation habitats were driven by nutrient content and salinity, showing clustering to similar bottom-up forces and dissimilarities in significantly different colonisation habitats.

Topsoil microbial community structure responds to land cover type and environmental zone in the Western Pacific region

Soil encompasses diverse microbial communities that are essential for fundamental ecosystem functions such as biogeochemical cycling. To better understand underlying biogeochemical processes, it is necessary to know the structure of soil archaeal and bacterial communities and their responses to edaphic and climate variables within and across various land cover types (LCTs) and environmental zones (ENZs). Here we sampled eighty-nine sites across five ENZs and four LCTs within the Western Pacific region. Through leveraging the second-generation sequencing of topsoil samples, we showed that α-diversity (taxonomic diversity) of archaea strongly varied within LCTs, whereas bacterial α-diversity was significantly controlled by both LCT and ENZ. Soil archaea and bacteria showed global niche differentiation associated with contrasting diversity responses to latitude and differential responses of microbial diversity patterns to edaphic and climate variables within LCTs and ENZs. In contrast to α-diversity, microbial β-diversity (the compositional dissimilarity between sites) was majorly governed by ENZs, particularly for archaea (P < 0.01). Our results highlight the importance of LCTs and ENZs for understanding soil microbial contributions to nutrient dynamics and ecosystem resilience under land-use intensification and climate change.

Microbiomes in forensic botany: a review

Fragments of botanical material can often be found at crime scenes (on live and dead bodies, or on incriminating objects) and can provide circumstantial evidence on various aspects of forensic investigations such as determining crime scene locations, times of death or possession of illegal species. Morphological and genetic analysis are the most commonly applied methods to analyze plant fragment evidence but are limited by their low capacity to differentiate between potential source locations, especially at local scales. Here, we review the current applications and limitations of current plant fragment analysis for forensic investigations and introduce the potential of microbiome analysis to complement the existing forensic plant fragment analysis toolkit. The potential for plant fragment provenance identification at geographic scales meaningful to forensic investigations warrants further investigation of the phyllosphere microbiome in this context. To that end we identify three key areas of future research: 1) Retrieval of microbial DNA of sufficient quality and quantity from botanical material; 2) Variability of the phyllosphere microbiome at different taxonomic and spatial scales, with explicit reference to assignment capacity; 3) Impacts on assignment capacity of time, seasonality and movement of fragments between locations. The development of robust microbiome analysis tools for forensic purposes in botanical material could increase the evidentiary value of the botanical evidence commonly encountered in casework, aiding in the identification of crime scene locations.

The Microbiome of Size-Fractionated Airborne Particles from the Sahara Region

Diverse airborne microbes affect human health and biodiversity, and the Sahara region of West Africa is a globally important source region for atmospheric dust. We collected size-fractionated (>10, 10-2.5, 2.5-1.0, 1.0-0.5, and <0.5 μm) atmospheric particles in Mali, West Africa and conducted the first cultivation-independent study of airborne microbes in this region using 16S rRNA gene sequencing. Abundant and diverse microbes were detected in all particle size fractions at levels higher than those previously hypothesized for desert regions. Average daily abundance was 1.94 × 10⁵ 16S rRNA copies/m³. Daily patterns in abundance for particles <0.5 μm differed significantly from other size fractions likely because they form mainly in the atmosphere and have limited surface resuspension. Particles >10 μm contained the greatest fraction of daily abundance (51-62%) and had significantly greater diversity than smaller particles. Greater bacterial abundance of particles >2.5 μm that are bigger than the average bacterium suggests that most airborne bacteria are present as aggregates or attached to particles rather than as free-floating cells. Particles >10 μm have very short atmospheric lifetimes and thus tend to have more localized origins. We confirmed the presence of several potential pathogens using polymerase chain reaction that are candidates for viability and strain testing in future studies. These species were detected on all particle sizes tested, including particles <2.5 μm that are expected to undergo long-range transport. Overall, our results suggest that the composition and sources of airborne microbes can be better discriminated by collecting size-fractionated samples.

Cyanobacteria and Algae in Clouds and Rain in the Area of puy de Dôme, Central France

The atmosphere contains diverse living microbes, of which the heterotrophic community has been the best studied. Microbes with other trophic modes, such as photoautotrophy, have received much less attention. In this study, culture-independent and dependent methods were used to examine the presence and diversity of oxygenic photoautotrophic microbes in clouds and rain collected at or around puy de Dôme Mountain, central France. Cloud water was collected from the summit of puy de Dôme (1,465 m above sea level [a.s.l.]) for cultivation and metagenomic analysis. Cyanobacteria, diatoms, green algae, and other oxygenic photoautotrophs were found to be recurrent members of clouds, while green algae affiliated with the Chlorellaceae were successfully cultured from three different clouds. Additionally, rain samples were collected below the mountain from Opme meteorological station (680 m a.s.l.). The abundance of chlorophyll a-containing cells and the diversity of cyanobacteria and green algae in rain were assessed by flow cytometry and amplicon sequencing. The corresponding downward flux of chlorophyll a-containing organisms to the ground, entering surface ecosystems with rain, varied with time and was estimated to be between ∼1 and >300 cells cm^-2 day^-1 during the sampling period. Besides abundant pollen from Pinales and Rosales, cyanobacteria of the Chroococcidiopsidales and green algae of the Trebouxiales were dominant in rain samples. Certain members of these taxa are known to be ubiquitous and stress tolerant and could use the atmosphere for dispersal. Overall, our results indicate that the atmosphere carries diverse, viable oxygenic photoautotrophic microbes and acts as a dispersal vector for this microbial guild.IMPORTANCE Information regarding the diversity and abundance of oxygenic photoautotrophs in the atmosphere is limited. More information from diverse locations is needed. These airborne organisms could have important impacts upon atmospheric processes and on the ecosystems they enter after deposition. Oxygenic photoautotrophic microbes are integral to ecosystem functioning, and some have the potential to affect human health. A better understanding of the diversity and the movements of these aeolian dispersed organisms is needed to understand their ecology, as well as how they could affect ecosystems and human health.

Silent rain: does the atmosphere-mediated connectivity between microbiomes influence bacterial evolutionary rates?

Air carries a vast number of bacteria and viruses over great distances all the time. This leads to continuous introduction of foreign genetic material to local, established microbial communities. In this perspective, I ask whether this silent rain may have a slowing effect on the overall evolutionary rates in the microbial biosphere. Arguably, the greater the genetic divergence between gene 'donors' and 'recipients', the greater the chance that the gene product has a deleterious epistatic interaction with other gene products in its genetic environment. This is due to the long-term absence of check for mutual compatibility. As such, if an organism is extensively different from other bacteria, genetic innovations are less probable to fit to the genome. Here, genetic innovation would be anything that elevates the fitness of the gene vehicle (e.g. bacterium) over its contemporaries. Adopted innovations increase the fitness of the compatible genome over incompatible ones, thus possibly tempering the pace at which mutations accumulate in existing genomes over generations. I further discuss the transfer of bacteriophages through atmosphere and potential effects that this may have on local dynamics and perhaps phage survival.

The effects of Bidens alba invasion on soil bacterial communities across different coastal ecosystem land-use types in southern China

Environments in both biotic and abiotic ecosystems have been affected by the colonization of non-native flora. In this study, we examined the effect of Bidens alba invasion on different land-use types along a coastline in southern China. Bacterial communities in each site were determined using 16S rDNA sequencing, and soil physicochemical properties were analyzed using standard methods. Although our results indicated that B. alba invasion did not have a significant effect on the alpha diversity of bacteria, it caused significant differences in soil bacterial community composition between invaded and uninvaded soil across different land-use types. Beta diversity and several physicochemical properties in forest, orchard and waterfront environments were recorded to be more susceptible to B. alba invasion. A high proportion of the variation of bacterial communities can be explained by a combination of environmental variables, indicating that environmental selection rather than plant invasion is a more effective process in coastal microbial assemblages. By comparing topological roles of shared OTUs among invaded and uninvaded soil, keystone taxa in invaded soil were identified. Acidobacteria was the major phyla involved in the invasive process which could be driven by environmental selection. How key phyla react in our experiment should be verified by further studies.

Diverse Bacterial Communities From Qaidam Basin of the Qinghai-Tibet Plateau: Insights Into Variations in Bacterial Diversity Across Different Regions

The Qaidam Basin of the Qinghai–Tibet Plateau is a cold, hyper-arid desert that presents extreme challenges to microbial communities. As little is known about variations between surface and subsurface microbial communities, high-throughput DNA sequencing was used in this study to profile bacterial communities of the soil samples collected at different depths in three regions in the Qaidam Basin. The α-diversity indices (Chao, Shannon, and Simpson) indicated that bacterial abundance and diversity were higher in the east and the high-elevation regions compared to the west region. In general, Firmicutes was dominant in the west region, while Proteobacteria and Acidobacteria were dominant in the east and the high-elevation regions. The structure of the bacterial communities differed greatly across regions, being strongly correlated with total organic carbon (TOC) and total nitrogen (TN) content. The differences in bacterial communities between the surface and the subsurface soil samples were smaller than the differences across the regions. Network analyses of environmental factors and bacterial genera indicated significant positive correlations in all regions. Overall, our study provides evidence that TOC and TN are the best predictors of both surface and subsurface bacterial communities across the Qaidam Basin. This study concludes that the bacterial community structure is influenced by both the spatial distance and the local environment, but environmental factors are the primary drivers of bacterial spatial patterns in the Qaidam Basin.

Airborne bacterial emission fluxes from manure-fertilized agricultural soil

This is the first study to quantify the dependence on wind velocity of airborne bacterial emission fluxes from soil. It demonstrates that manure bacteria get aerosolized from fertilized soil more easily than soil bacteria, and it applies bacterial genomic sequencing for the first time to trace environmental faecal contamination back to its source in the chicken barn. We report quantitative, airborne emission fluxes of bacteria during and following the fertilization of agricultural soil with manure from broiler chickens. During the fertilization process, the concentration of airborne bacteria culturable on blood agar medium increased more than 600 000-fold, and 1 m3 of air carried 2.9 × 105 viable enterococci, i.e. indicators of faecal contamination which had been undetectable in background air samples. Trajectory modelling suggested that atmospheric residence times and dispersion pathways were dependent on the time of day at which fertilization was performed. Measurements in a wind tunnel indicated that airborne bacterial emission fluxes from freshly fertilized soil under local climatic conditions on average were 100-fold higher than a previous estimate of average emissions from land. Faecal bacteria collected from soil and dust up to seven weeks after fertilization could be traced to their origins in the poultry barn by genomic sequencing. Comparative analyses of 16S rRNA gene sequences from manure, soil and dust showed that manure bacteria got aerosolized preferably, likely due to their attachment to low-density manure particles. Our data show that fertilization with manure may cause substantial increases of bacterial emissions from agricultural land. After mechanical incorporation of manure into soil, however, the associated risk of airborne infection is low.

Airborne bacteria confirm the pristine nature of the Southern Ocean boundary layer

We found that the summer airborne bacterial community in the marine boundary layer over the Southern Ocean directly south of Australia is dominated by marine bacteria emitted in sea spray, originating primarily from the west in a zonal band at the latitude of collection. We found that airborne communities were more diverse to the north, and much less so toward Antarctica. These results imply that sea spray sources largely control the number concentrations of nuclei for liquid cloud droplets and limit ice nucleating particle concentrations to the low values expected in nascent sea spray. In the sampled region, the sources of summer cloud-active particles therefore are unlikely to have changed in direct response to perturbations in continental anthropogenic emissions.

Microorganisms are ubiquitous and highly diverse in the atmosphere. Despite the potential impacts of airborne bacteria found in the lower atmosphere over the Southern Ocean (SO) on the ecology of Antarctica and on marine cloud phase, no previous region-wide assessment of bioaerosols over the SO has been reported. We conducted bacterial profiling of boundary layer shipboard aerosol samples obtained during an Austral summer research voyage, spanning 42.8 to 66.5°S. Contrary to findings over global subtropical regions and the Northern Hemisphere, where transport of microorganisms from continents often controls airborne communities, the great majority of the bacteria detected in our samples were marine, based on taxonomy, back trajectories, and source tracking analysis. Further, the beta diversity of airborne bacterial communities varied with latitude and temperature, but not with other meteorological variables. Limited meridional airborne transport restricts southward community dispersal, isolating Antarctica and inhibiting microorganism and nutrient deposition from lower latitudes to these same regions. A consequence and implication for this region’s marine boundary layer and the clouds that overtop it is that it is truly pristine, free from continental and anthropogenic influences, with the ocean as the dominant source controlling low-level concentrations of cloud condensation nuclei and ice nucleating particles.

Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection

Polluted air poses a significant threat to human health. Exposure to particulate matter (PM) and harmful gases contributes to cardiovascular and respiratory diseases, including allergies and obstructive lung disease. Air pollution may also be linked to cancer and reduced life expectancy. Uptake of PM has been shown to cause pathological changes in the intestinal microbiota in mice and humans. Less is known about the effects of pollution-associated microbiota on human health. Several recent studies described the microbiomes of urban and rural air samples, of the stratosphere and sand particles, which can be transported over long distances, as well as the air of indoor environments. Here, we summarize the current knowledge on airborne bacterial, viral, and fungal communities and discuss their potential consequences on human health. The current data suggest that bacterial pathogens are typically too sparse and short-lived in air to pose a significant risk for infecting healthy people. However, airborne fungal spores may exacerbate allergies and asthma. Little information is available on viruses including phages, and future studies are likely to detect known and novel viruses with a yet unknown impact on human health. Furthermore, varying experimental protocols have been employed in the recent microbiome and virome studies. Therefore, standardized methodologies will be required to allow for better comparisons between studies. Air pollution has been linked to more severe outcomes of SARS (severe acute respiratory syndrome) coronavirus (SARS-CoV) infections. This may have contributed to severe SARS-CoV-2 outbreaks, especially those in China, Northern Italy, Iran, and New York City.

Impacts of Saharan Dust Intrusions on Bacterial Communities of the Low Troposphere

We have analyzed the bacterial community of a large Saharan dust event in the Iberian Peninsula and, for the first time, we offer new insights regarding the bacterial distribution at different altitudes of the lower troposphere and the replacement of the microbial airborne structure as the dust event receeds. Samples from different open-air altitudes (surface, 100 m and 3 km), were obtained onboard the National Institute for Aerospace Technology (INTA) C-212 aircrafts. Samples were collected during dust and dust-free air masses as well two weeks after the dust event. Samples related in height or time scale seems to show more similar community composition patterns compared with unrelated samples. The most abundant bacterial species during the dust event, grouped in three different phyla: (a) Proteobacteria: Rhizobiales, Sphingomonadales, Rhodobacterales, (b) Actinobacteria: Geodermatophilaceae; (c) Firmicutes: Bacillaceae. Most of these taxa are well known for being extremely stress-resistant. After the dust intrusion, Rhizobium was the most abundant genus, (40-90% total sequences). Samples taken during the flights carried out 15 days after the dust event were much more similar to the dust event samples compared with the remaining samples. In this case, Brevundimonas, and Methylobacterium as well as Cupriavidus and Mesorizobium were the most abundant genera.

Bacteria and archaea on Earth and their abundance in biofilms

Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 10³⁰ cells) exist in the 'big five' habitats: deep oceanic subsurface (4 × 10²⁹), upper oceanic sediment (5 × 10²⁸), deep continental subsurface (3 × 10²⁹), soil (3 × 10²⁹) and oceans (1 × 10²⁹). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20-80% of cells in the subsurface exist as biofilms. Hence, overall, 40-80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.

Air mass source determines airborne microbial diversity at the ocean-atmosphere interface of the Great Barrier Reef marine ecosystem

The atmosphere is the least understood biome on Earth despite its critical role as a microbial transport medium. The influence of surface cover on composition of airborne microbial communities above marine systems is unclear. Here we report evidence for a dynamic microbial presence at the ocean-atmosphere interface of a major marine ecosystem, the Great Barrier Reef, and identify that recent air mass trajectory over an oceanic or continental surface associated with observed shifts in airborne bacterial and fungal diversity. Relative abundance of shared taxa between air and coral microbiomes varied between 2.2 and 8.8% and included those identified as part of the core coral microbiome. We propose that this variable source of atmospheric inputs may in part contribute to the diverse and transient nature of the coral microbiome.

Large-scale distribution of bacterial communities in the Qaidam Basin of the Qinghai-Tibet Plateau

Many studies have investigated patterns of soil microbial communities over large spatial scales. However, these studies mainly focused on a few sites. Here, we studied the near‐surface (0–30 cm) soil microbial communities of 35 soil samples collected from most of the areas of the Qaidam Basin, which is the largest basin on the Qinghai–Tibet Plateau. A total of 32 phyla and 838 genera were detected from all the samples, in which Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were the most dominant and cosmopolitan phyla. The most abundant phyla (relative abundance > 5%) detected in all 35 soil samples were also the most dominant, which could be explained by their great dispersal ability. The microbial community structures correlated strongly with variations in pH and Mg²⁺ and were distinct between the high Mg²⁺ content (>20 g/kg) samples and other samples (Acidobacteria, Actinobacteria, and Chloroflexi were significantly less abundant in the high Mg²⁺ content group, but the abundance of Firmicutes was significantly greater). Finally, the microbial spatial pattern was influenced by both the local environment and spatial distance, but environmental factors were the primary drivers of microbial spatial patterns in the Qaidam Basin.

Seasonal Changes of Airborne Bacterial Communities Over Tokyo and Influence of Local Meteorology

In order to study airborne bacterial community dynamics over Tokyo, including fine-scale correlations between airborne microorganisms and meteorological conditions, and the influence of local versus long-range transport of microbes, air samples were collected on filters for periods ranging from 48 to 72 h. The diversity of the microbial community was assessed by next generation sequencing. Predicted source regions of airborne particles, from back trajectory analyses, changed abruptly from the Pacific Ocean to the Eurasian Continent in the beginning of October. However, the microbial community composition and the alpha and beta diversities were not affected by this shift in meteorological regime, suggesting that long-range transport from oceanic or continental sources was not the principal determinant controlling the local airborne microbiome. By contrast, we found a significant correlation between the local meteorology, especially relative humidity and wind speed, and both alpha diversity and beta diversity. Among four potential local source categories (soil, bay seawater, river, and pond), bay seawater and soil were identified as constant and predominant sources. Statistical analyses point toward humidity as the most influential meteorological factor, most likely because it is correlated with soil moisture and hence negatively correlated with the dispersal of particles from the land surface. In this study, we have demonstrated the benefits of fine-scale temporal analyses for understanding the sources and relationships with the meteorology of Tokyo's "aerobiome."

Seasonal Changes of Airborne Bacterial Communities Over Tokyo and Influence of Local Meteorology

In order to study airborne bacterial community dynamics over Tokyo, including fine-scale correlations between airborne microorganisms and meteorological conditions, and the influence of local versus long-range transport of microbes, air samples were collected on filters for periods ranging from 48 to 72 h. The diversity of the microbial community was assessed by next generation sequencing. Predicted source regions of airborne particles, from back trajectory analyses, changed abruptly from the Pacific Ocean to the Eurasian Continent in the beginning of October. However, the microbial community composition and the alpha and beta diversities were not affected by this shift in meteorological regime, suggesting that long-range transport from oceanic or continental sources was not the principal determinant controlling the local airborne microbiome. By contrast, we found a significant correlation between the local meteorology, especially relative humidity and wind speed, and both alpha diversity and beta diversity. Among four potential local source categories (soil, bay seawater, river, and pond), bay seawater and soil were identified as constant and predominant sources. Statistical analyses point toward humidity as the most influential meteorological factor, most likely because it is correlated with soil moisture and hence negatively correlated with the dispersal of particles from the land surface. In this study, we have demonstrated the benefits of fine-scale temporal analyses for understanding the sources and relationships with the meteorology of Tokyo’s “aerobiome.”

Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states

The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity. The communities consisted of 1.3×103 ± 1.0×103 cells m-3, which were aerosolized from local terrestrial environments or transported from marine, glaciated and terrestrial surfaces over long distances. On average, airborne bacterial cells displayed a high activity potential, reflected in the high 16S rRNA copy number (590 ± 300 rRNA cell-1), that correlated positively with water vapor pressure. We observed that bacterial clades differed in their activity potential. For instance, a high activity potential was seen for Rubrobacteridae and Clostridiales, while a low activity potential was observed for Proteobacteria. Of those bacterial families that harbor ice-nucleation active species, which are known to facilitate freezing and may thus be involved in cloud and rain formation, cells with a high activity potential were rare in air, but were enriched in rain.

Solar UV radiation and microbial life in the atmosphere

Many microorganisms are alive while suspended in the atmosphere, and some seem to be metabolically active during their time there. One of the most important factors threatening their life and activity is solar ultraviolet (UV) radiation. Quantitative understanding of the spatial and temporal survival patterns in the atmosphere, and of the ultimate deposition of microbes to the surface, is limited by a number factors some of which are discussed here. These include consideration of appropriate spectral sensitivity functions for biological damage (e.g. inactivation), and the estimation of UV radiation impingent on a microorganism suspended in the atmosphere. We show that for several bacteria (E. coli, S. typhimurium, and P. acnes) the inactivation rates correlate well with irradiances weighted by the DNA damage spectrum in the UV-B spectral range, but when these organisms show significant UV-A (or visible) sensitivities, the correlations become clearly non-linear. The existence of these correlations enables the use of a single spectrum (here DNA damage) as a proxy for sensitivity spectra of other biological effects, but with some caution when the correlations are strongly non-linear. The radiative quantity relevant to the UV exposure of a suspended particle is the fluence rate at an altitude above ground, while down-welling irradiance at ground-level is the quantity most commonly measured or estimated in satellite-derived climatologies. Using a radiative transfer model that computes both quantities, we developed a simple parameterization to exploit the much larger irradiance data bases to estimate fluence rates, and present the first fluence-rate based climatology of DNA-damaging UV radiation in the atmosphere. The estimation of fluence rates in the presence of clouds remains a particularly challenging problem. Here we note that both reductions and enhancements in the UV radiation field are possible, depending mainly on cloud optical geometry and prevailing solar zenith angles. These complex effects need to be included in model simulations of the atmospheric life cycle of the organisms.

Biogeography of soil bacteria and archaea across France

Over the last two decades, a considerable effort has been made to decipher the biogeography of soil microbial communities as a whole, from small to broad scales. In contrast, few studies have focused on the taxonomic groups constituting these communities; thus, our knowledge of their ecological attributes and the drivers determining their composition and distribution is limited. We applied a pyrosequencing approach targeting 16S ribosomal RNA (rRNA) genes in soil DNA to a set of 2173 soil samples from France to reach a comprehensive understanding of the spatial distribution of bacteria and archaea and to identify the ecological processes and environmental drivers involved. Taxonomic assignment of the soil 16S rRNA sequences indicated the presence of 32 bacterial phyla or subphyla and 3 archaeal phyla. Twenty of these 35 phyla were cosmopolitan and abundant, with heterogeneous spatial distributions structured in patches ranging from a 43- to 260-km radius. The hierarchy of the main environmental drivers of phyla distribution was soil pH > land management > soil texture > soil nutrients > climate. At a lower taxonomic level, 47 dominant genera belonging to 12 phyla aggregated 62.1% of the sequences. We also showed that the phylum-level distribution can be determined largely by the distribution of the dominant genus or, alternatively, reflect the combined distribution of all of the phylum members. Together, our study demonstrated that soil bacteria and archaea present highly diverse biogeographical patterns on a nationwide scale and that studies based on intensive and systematic sampling on a wide spatial scale provide a promising contribution for elucidating soil biodiversity determinism.

Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days

The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM_2.5 [<2.5 μm], PM₁₀ [<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions (R = 0.157, P < 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus, Tumebacillus, and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO₂ concentration, relative humidity, PM₁₀ concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM₁₀ samples (Dokdonella, Caenimonas, Geminicoccus, and Sphingopyxis) and PM_2.5 samples (Cellulomonas and Rhizobacter), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus, Kocuria, and Sphingomonas Network analysis indicated that Paracoccus, Rubellimicrobium, Kocuria, and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days.IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus, Tumebacillus, and Desulfurispora) increased significantly on heavy-haze days. In addition, Paracoccus, Rubellimicrobium, Kocuria, and Arthrobacter were the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze.

Effect of air pollution on the total bacteria and pathogenic bacteria in different sizes of particulate matter

In recent years, air pollution events have occurred frequently in China during the winter. Most studies have focused on the physical and chemical composition of polluted air. Some studies have examined the bacterial bioaerosols both indoors and outdoors. But few studies have focused on the relationship between air pollution and bacteria, especially pathogenic bacteria. Airborne PM samples with different diameters and different air quality index values were collected in Hangzhou, China from December 2014 to January 2015. High-throughput sequencing of 16S rRNA was used to categorize the airborne bacteria. Based on the NCBI database, the "Human Pathogen Database" was established, which is related to human health. Among all the PM samples, the diversity and concentration of total bacteria were lowest in the moderately or heavily polluted air. However, in the PM2.5 and PM10 samples, the relative abundances of pathogenic bacteria were highest in the heavily and moderately polluted air respectively. Considering the PM samples with different particle sizes, the diversities of total bacteria and the proportion of pathogenic bacteria in the PM10 samples were different from those in the PM2.5 and TSP samples. The composition of PM samples with different sizes range may be responsible for the variances. The relative humidity, carbon monoxide and ozone concentrations were the main factors, which affected the diversity of total bacteria and the proportion of pathogenic bacteria. Among the different environmental samples, the compositions of the total bacteria were very similar in all the airborne PM samples, but different from those in the water, surface soil, and ground dust samples. Which may be attributed to that the long-distance transport of the airflow may influence the composition of the airborne bacteria. This study of the pathogenic bacteria in airborne PM samples can provide a reference for environmental and public health researchers.

Variation in range size and dispersal capabilities of microbial taxa

Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes. However, contrary to expectations, those microbial taxa that were locally abundant did not necessarily have larger range sizes. The observed differences in microbial range sizes were generally predictable from taxonomic identity, phenotypic traits, genomic attributes, and habitat preferences, findings that provide insight into the factors shaping patterns of microbial biogeography.

Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity

In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.

Transmission of Bacterial Endophytes

Plants are hosts to complex communities of endophytic bacteria that colonize the interior of both below- and aboveground tissues. Bacteria living inside plant tissues as endophytes can be horizontally acquired from the environment with each new generation, or vertically transmitted from generation to generation via seed. A better understanding of bacterial endophyte transmission routes and modes will benefit studies of plant–endophyte interactions in both agricultural and natural ecosystems. In this review, we provide an overview of the transmission routes that bacteria can take to colonize plants, including vertically via seeds and pollen, and horizontally via soil, atmosphere, and insects. We discuss both well-documented and understudied transmission routes, and identify gaps in our knowledge on how bacteria reach the inside of plants. Where little knowledge is available on endophytes, we draw from studies on bacterial plant pathogens to discuss potential transmission routes. Colonization of roots from soil is the best studied transmission route, and probably the most important, although more studies of transmission to aerial parts and stomatal colonization are needed, as are studies that conclusively confirm vertical transfer. While vertical transfer of bacterial endophytes likely occurs, obligate and strictly vertically transferred symbioses with bacteria are probably unusual in plants. Instead, plants appear to benefit from the ability to respond to a changing environment by acquiring its endophytic microbiome anew with each generation, and over the lifetime of individuals.